{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T21:25:45Z","timestamp":1774905945328,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2018,12,3]],"date-time":"2018-12-03T00:00:00Z","timestamp":1543795200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"crossref","award":["150654"],"award-info":[{"award-number":["150654"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"crossref","award":["BB\/M015009\/1"],"award-info":[{"award-number":["BB\/M015009\/1"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative genomic analyses. As provided by several orthology databases, hierarchical orthologous groups (HOGs) are sets of genes that are inferred to have descended from a common ancestral gene within a species clade. This implies that the set of HOGs defined for a particular clade correspond to the ancestral genes found in its last common ancestor. Furthermore, by keeping track of HOG composition along the species tree, it is possible to infer the emergence, duplications and losses of genes within a gene family of interest. However, the lack of tools to manipulate and analyse HOGs has made it difficult to extract, display and interpret this type of information. To address this, we introduce interactive HOG analysis method, an interactive JavaScript widget to visualize and explore gene family history encoded in HOGs and python HOG analysis method, a python library for programmatic processing of genes families. These complementary open source tools greatly ease adoption of HOGs as a scalable and interpretable concept to relate genes across multiple species.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>iHam\u2019s code is available at https:\/\/github.com\/DessimozLab\/iHam or can be loaded dynamically. pyHam\u2019s code is available at https:\/\/github.com\/DessimozLab\/pyHam and or via the pip package \u2018pyham\u2019.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty994","type":"journal-article","created":{"date-parts":[[2018,11,30]],"date-time":"2018-11-30T20:11:59Z","timestamp":1543608719000},"page":"2504-2506","source":"Crossref","is-referenced-by-count":38,"title":["iHam and pyHam: visualizing and processing hierarchical orthologous groups"],"prefix":"10.1093","volume":"35","author":[{"given":"Cl\u00e9ment-Marie","family":"Train","sequence":"first","affiliation":[{"name":"SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Zurich, Switzerland"},{"name":"Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Miguel","family":"Pignatelli","sequence":"additional","affiliation":[{"name":"Open Targets"},{"name":"EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adrian","family":"Altenhoff","sequence":"additional","affiliation":[{"name":"SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"},{"name":"ETH Zurich, Department of Computer Science, Zurich, Switzerland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2170-853X","authenticated-orcid":false,"given":"Christophe","family":"Dessimoz","sequence":"additional","affiliation":[{"name":"SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"},{"name":"Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland"},{"name":"Department of Computational Biology, University of Lausanne, Lausanne, Switzerland"},{"name":"Department of Genetics, Evolution and Environment, University College London, London, UK"},{"name":"Department of Computer Science, University College London, London, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,12,3]]},"reference":[{"key":"2023062712302152800_bty994-B1","doi-asserted-by":"crossref","first-page":"D477","DOI":"10.1093\/nar\/gkx1019","article-title":"The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces","volume":"46","author":"Altenhoff","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023062712302152800_bty994-B2","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1093\/bioinformatics\/btv625","article-title":"Berry SylvX: a viewer for phylogenetic tree reconciliations","volume":"32","author":"Chevenet","year":"2016","journal-title":"Bioinformatics"},{"key":"2023062712302152800_bty994-B3","doi-asserted-by":"crossref","first-page":"2596","DOI":"10.1093\/bioinformatics\/bti325","article-title":"Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases","volume":"21","author":"Dufayard","year":"2005","journal-title":"Bioinformatics"},{"key":"2023062712302152800_bty994-B4","doi-asserted-by":"crossref","first-page":"99","DOI":"10.2307\/2412448","article-title":"Distinguishing homologous from analogous proteins","volume":"19","author":"Fitch","year":"1970","journal-title":"Syst. 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